Hi all!
I have one question about the variant filtering with the useful ANNOVAR software.
I prepare my input in this way:
And then I'm filtering with this argument:
When revising the output I find entries like this... (summarized to avoid disturbing):
1000g2012apr_all 0.04 chr1 21573855 21573855 G A chr1 21573855 rs1076669 G A .................
1000g2012apr_all 0.99 chr1 236882303 236882303 T C chr1 236882303 rs1341864 T C .................
1000g2012apr_all 0.01 chr11 47371578 47371578 G A chr11 47371578 rs3218719 G A .................
...and more...
Why some of the variants have MAFs bigger than 0.05?
Thank you all in advance...
I have one question about the variant filtering with the useful ANNOVAR software.
I prepare my input in this way:
Code:
$ perl convert2annovar.pl -format vcf4 ~/Desktop/MySample.vcf --allsample -comment -include -outfile ~/Desktop/MySample.avinput
Code:
$ perl annotate_variation.pl -filter -dbtype 1000g2012apr_all ~/Desktop/MySample.avinput humandb/ -maf_threshold 0.05 -buildver hg19 --comment -reverse -outfile ~/Desktop/MySample_MAF005_1000G
1000g2012apr_all 0.04 chr1 21573855 21573855 G A chr1 21573855 rs1076669 G A .................
1000g2012apr_all 0.99 chr1 236882303 236882303 T C chr1 236882303 rs1341864 T C .................
1000g2012apr_all 0.01 chr11 47371578 47371578 G A chr11 47371578 rs3218719 G A .................
...and more...
Why some of the variants have MAFs bigger than 0.05?
Thank you all in advance...
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